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Yorodumi- PDB-9cwl: Crystal structure of outer membrane lipoprotein carrier protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cwl | |||||||||
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Title | Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (monoclinic P Form) | |||||||||
Components | Outer membrane lipocarrier LolA family protein | |||||||||
Keywords | LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / lipoprotein carrier / LolA | |||||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA-like / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / protein transport / metal ion binding / Outer membrane lipocarrier LolA family protein Function and homology information | |||||||||
Biological species | Francisella philomiragia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia (monoclinic P Form) Authors: Lovell, S. / Taylor, K.E. / Cooper, A. / Battaile, K.P. / Buchko, G.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cwl.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cwl.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 9cwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cwl_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 9cwl_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 9cwl_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 9cwl_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/9cwl ftp://data.pdbj.org/pub/pdb/validation_reports/cw/9cwl | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22194.951 Da / Num. of mol.: 1 / Fragment: L32-N205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella philomiragia (bacteria) / Gene: Fphi_1079 / Plasmid: FrphA.20731.a.VL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0TX44 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus A9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2. FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well A9 drop2, Puck: ...Details: Morpheus A9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2. FrphA.20731.a.VL2.PB00125 at 13.9 mg/mL. plate 14180 well A9 drop2, Puck: PSL0911 and PSL0912 merged, Cryo: Direct |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 27, 2024 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.96 Å / Num. obs: 14044 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.065 / Rrim(I) all: 0.165 / Χ2: 1.03 / Net I/σ(I): 9.8 / Num. measured all: 92640 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.696 / Num. measured all: 5816 / Num. unique obs: 855 / CC1/2: 0.719 / Rpim(I) all: 0.707 / Rrim(I) all: 1.839 / Χ2: 0.92 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.96 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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